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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $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' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ), 'gf_id' => 'HOM05D001445', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001445' ), 'data_identifier' => 'HOM05D001445', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001445', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '436', 'num_species' => '87' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p30180' => 'bna', 'A02p30500' => 'bna', 'A02p30550' => 'bna', 'A02p30560' => 'bna', 'A02p30580' => 'bna', 'A02p30590' => 'bna', 'A02p30600' => 'bna', 'A06p45450' => 'bna', 'A06p45680' => 'bna', 'A07p19800' => 'bna', 'A09p22680' => 'bna', 'A09p22690' => 'bna', 'A09p22700' => 'bna', 'Aa31LG9G17000' => 'aar', 'Aa31LG9G5990' => 'aar', 'Aa31sc241G40' => 'aar', 'Aa31sc241G60' => 'aar', 'Actinidia03398' => 'ach', 'Actinidia03399' => 'ach', 'Actinidia21612' => 'ach', 'Actinidia25936' => 'ach', 'Actinidia30953' => 'ach', 'Ah.01g010410' => 'amhyb', 'Ah.05g179460' => 'amhyb', 'Ah.07g199410' => 'amhyb', 'Ah.09g229110' => 'amhyb', 'AL7G51920' => 'aly', 'AL8G11310' => 'aly', 'AL8G11320' => 'aly', 'AL8G11330' => 'aly', 'AL8G11340' => 'aly', 'Aqoxy2G03058' => 'aox', 'Aqoxy2G03061' => 'aox', 'Aqoxy2G03062' => 'aox', 'Aqoxy2G03063' => 'aox', 'Aqoxy3G02555' => 'aox', 'Aqoxy3G02557' => 'aox', 'Aqoxy5G00072' => 'aox', 'Aqoxy5G03637' => 'aox', 'Aqoxy5G03639' => 'aox', 'Aqoxy7G04181' => 'aox', 'AT5G38610' => 'ath', 'AT5G46930' => 'ath', 'AT5G46940' => 'ath', 'AT5G46950' => 'ath', 'AT5G46960' => 'ath', 'AT5G46970' => 'ath', 'ATR0693G013' => 'atr', 'ATR0693G401' => 'atr', 'Atru.chr5.42' => 'acertr', 'Atru.chr5.72' => 'acertr', 'Atru.chr6.1791' => 'acertr', 'AUR62007212' => 'cqu', 'AUR62025289' => 'cqu', 'BcaB01g05448' => 'bca', 'BcaB02g08000' => 'bca', 'BcaB07g30804' => 'bca', 'BcaB07g30808' => 'bca', 'BcaB08g36203' => 'bca', 'BcaC01g02648' => 'bca', 'BcaC03g16868' => 'bca', 'BcaC03g16906' => 'bca', 'BcaC03g16912' => 'bca', 'BcaC03g16913' => 'bca', 'BcaC04g21666' => 'bca', 'BcaC04g21667' => 'bca', 'BcaC06g31431' => 'bca', 'BcaC06g31448' => 'bca', 'BcaC06g34307' => 'bca', 'BcaC08g44398' => 'bca', 'BolC2t10801H' => 'bol', 'BolC2t10840H' => 'bol', 'BolC2t10846H' => 'bol', 'BolC2t10847H' => 'bol', 'BolC3t18500H' => 'bol', 'BolC6t37042H' => 'bol', 'BolC7t43593H' => 'bol', 'BolC9t55774H' => 'bol', 'BolC9t55775H' => 'bol', 'BraA02t08034Z' => 'bra', 'BraA02t08068Z' => 'bra', 'BraA02t08073Z' => 'bra', 'BraA02t08076Z' => 'bra', 'BraA02t08077Z' => 'bra', 'BraA02t08078Z' => 'bra', 'BraA06t27413Z' => 'bra', 'BraA06t27437Z' => 'bra', 'BraA07t29681Z' => 'bra', 'BraA09t37873Z' => 'bra', 'BraA09t37874Z' => 'bra', 'C02p47650' => 'bna', 'C02p48090' => 'bna', 'C02p48140' => 'bna', 'C02p48150' => 'bna', 'C03p62420' => 'bna', 'C06p18290' => 'bna', 'C07p30520' => 'bna', 'C09p29170' => 'bna', 'C09p29180' => 'bna', 'CAN.G572.46' => 'can', 'CAN.G572.48' => 'can', 'CAN.G572.49' => 'can', 'CAN.G756.16' => 'can', 'CANSAT21G0328' => 'cansat', 'CANSAT21G0723' => 'cansat', 'CANSAT25G2716' => 'cansat', 'CANSAT56G1763' => 'cansat', 'CANSAT56G2517' => 'cansat', 'CARHR089510' => 'chi', 'CARHR174480' => 'chi', 'CARHR174490' => 'chi', 'CARHR174500' => 'chi', 'CARHR174510' => 'chi', 'CARHR214060' => 'chi', 'Carub.0007s3724' => 'cru', 'Carub.0008s0089' => 'cru', 'Carub.0008s0090' => 'cru', 'Carub.0008s0091' => 'cru', 'Carub.0008s0092' => 'cru', 'Ca_22037_v3' => 'car', 'Ca_22038_v3' => 'car', 'Cc02_g25640' => 'ccan', 'Cc08_g01760' => 'ccan', 'CDE04G0621' => 'cde', 'CDE06G1635' => 'cde', 'CDE06G2513' => 'cde', 'CDE07G0552' => 'cde', 'CDE07G1929' => 'cde', 'CDE12G0631' => 'cde', 'Cfa011022' => 'cfa', 'Ciclev10023652m.g' => 'ccl', 'Ciclev10032808m.g' => 'ccl', 'Ciclev10033644m.g' => 'ccl', 'CiPaw.11G087100' => 'cil', 'CiPaw.13G022000' => 'cil', 'CiPaw.14G016700' => 'cil', 'ClCG00G004560' => 'cla', 'ClCG06G000830' => 'cla', 'ClCG06G000840' => 'cla', 'ClCG06G000850' => 'cla', 'ClCG06G016040' => 'cla', 'COL.COLO4_12351' => 'col', 'COL.COLO4_17125' => 'col', 'COL.COLO4_17126' => 'col', 'COL.COLO4_17127' => 'col', 'COL.COLO4_17128' => 'col', 'Cpa.g.sc29.3' => 'cpa', 'Cpa.g.sc52.68' => 'cpa', 'Cpa.g.sc52.69' => 'cpa', 'CsaV3_1G002510' => 'csa', 'CsaV3_3G010420' => 'csa', 'CsaV3_3G049590' => 'csa', 'CsaV3_6G006700' => 'csa', 'CSS0012427' => 'camsi', 'CSS0012481' => 'camsi', 'CSS0020469' => 'camsi', 'CSS0045791' => 'camsi', 'DCAR_025024' => 'dca', 'Dinv25174' => 'din', 'Dinv28905' => 'din', 'Dinv44021' => 'din', 'Duzib084G0732' => 'dzi', 'Duzib084G0977' => 'dzi', 'Duzib133G0634' => 'dzi', 'Duzib205G0415' => 'dzi', 'Duzib205G1605' => 'dzi', 'ECA234G4250' => 'eca', 'ECA236G4359' => 'eca', 'EL10Ac1g00256' => 'bvu', 'EL10Ac5g12203' => 'bvu', 'EL10Ac5g12204' => 'bvu', 'EL10Ac8g19001' => 'bvu', 'EL10Ac8g19002' => 'bvu', 'Eucgr.C00759' => 'egr', 'Eucgr.D01174' => 'egr', 'Eucgr.D01179' => 'egr', 'Eucgr.D01180' => 'egr', 'Eucgr.D01181' => 'egr', 'Eucgr.D01182' => 'egr', 'Eucgr.E00321' => 'egr', 'Eucgr.E01452' => 'egr', 'Eucgr.L01654' => 'egr', 'Eucgr.L02459' => 'egr', 'FAN01G2621' => 'fan', 'FAN03G2044' => 'fan', 'FAN04G1716' => 'fan', 'FAN06G3435' => 'fan', 'FAN08G0902' => 'fan', 'FAN08G1111' => 'fan', 'FAN08G3072' => 'fan', 'FAN10G1969' => 'fan', 'FAN10G3032' => 'fan', 'FAN13G3027' => 'fan', 'FAN18G2022' => 'fan', 'FAN18G2178' => 'fan', 'FAN18G4149' => 'fan', 'FAN18G4518' => 'fan', 'FvH4_5g20930' => 'fve', 'FvH4_5g20940' => 'fve', 'FvH4_5g20950' => 'fve', 'FvH4_5g21030' => 'fve', 'FvH4_7g08770' => 'fve', 'Glyma.03G103400' => 'gma', 'Glyma.05G068700' => 'gma', 'Glyma.05G068800' => 'gma', 'Glyma.17G044900' => 'gma', 'Glyma.17G151200' => 'gma', 'Glyma.17G151500' => 'gma', 'Gohir.A07G126650' => 'ghi', 'Gohir.A07G126700' => 'ghi', 'Gohir.A08G140800' => 'ghi', 'Gohir.A09G197900' => 'ghi', 'Gohir.A09G237400' => 'ghi', 'Gohir.D03G169433' => 'ghi', 'Gohir.D07G130800' => 'ghi', 'Gohir.D07G130850' => 'ghi', 'Gohir.D07G130900' => 'ghi', 'Gohir.D08G161800' => 'ghi', 'Gohir.D09G192500' => 'ghi', 'Gohir.D12G119500' => 'ghi', 'Gorai.001G141600' => 'gra', 'Gorai.001G141700' => 'gra', 'Gorai.001G141800' => 'gra', 'Gorai.001G141900' => 'gra', 'Gorai.003G179700' => 'gra', 'Gorai.004G168200' => 'gra', 'Gorai.006G215400' => 'gra', 'Gorai.006G261000' => 'gra', 'Gorai.008G130000' => 'gra', 'HanXRQChr04g0115481' => 'han', 'HanXRQChr07g0188521' => 'han', 'HanXRQChr16g0522931' => 'han', 'Haze_02903' => 'cav', 'Hma1.2p1_0173F.1_g076520' => 'hma', 'Hma1.2p1_0311F.1_g121170' => 'hma', 'Hma1.2p1_0311F.1_g121180' => 'hma', 'Hma1.2p1_0414F.1_g147630' => 'hma', 'HPP92_014651' => 'vpl', 'HPP92_015140' => 'vpl', 'HPP92_021578' => 'vpl', 'HPP92_021602' => 'vpl', 'HPP92_025709' => 'vpl', 'Lalb_Chr07g0181461' => 'lal', 'Lalb_Chr11g0066641' => 'lal', 'Lalb_Chr12g0210341' => 'lal', 'Lalb_Chr16g0386171' => 'lal', 'Lj2P248T28' => 'lonja', 'Lj3g0025567' => 'lja', 'Lj4g0000385' => 'lja', 'Lj4g0015413' => 'lja', 'Lj4g0026234' => 'lja', 'Lsat_1_v5_gn_4_38540' => 'lsa', 'Lsat_1_v5_gn_7_11841' => 'lsa', 'Manes.05G058600' => 'mes', 'Manes.08G115700' => 'mes', 'Manes.08G115800' => 'mes', 'Manes.15G171900' => 'mes', 'MBI04_g03340_MAGBIO' => 'mbi', 'MBI18_g25078_MAGBIO' => 'mbi', 'MBI18_g25092_MAGBIO' => 'mbi', 'MD02G1225200' => 'mdo', 'MD06G1041900' => 'mdo', 'MD06G1042400' => 'mdo', 'MD07G1088700' => 'mdo', 'Medtr4g099010' => 'mtr', 'Medtr8g009300' => 'mtr', 'MELO3C003367.2' => 'cme', 'MELO3C006266.2' => 'cme', 'MELO3C017187.2' => 'cme', 'MELO3C022456.2' => 'cme', 'MELO3C022457.2' => 'cme', 'MELO3C022458.2' => 'cme', 'Migut.B01486' => 'egut', 'Migut.N01714' => 'egut', 'MSTRG.17105' => 'ama', 'MSTRG.17106' => 'ama', 'MSTRG.20662' => 'ama', 'MSTRG.4961' => 'ama', 'Nitab4.5_0004088g0040' => 'nta', 'Nitab4.5_0005034g0010' => 'nta', 'Nitab4.5_0008694g0020' => 'nta', 'Nn1g00650' => 'nnu', 'Nn1g00653' => 'nnu', 'Nn1g00654' => 'nnu', 'Nn1g00663' => 'nnu', 'Nn1g00664' => 'nnu', 'Nn1g02148' => 'nnu', 'Nn5g27880' => 'nnu', 'Oeu002900.1' => 'oeu', 'Oeu018160.1' => 'oeu', 'Oeu024389.1' => 'oeu', 'Oeu024391.1' => 'oeu', 'Oeu024392.1' => 'oeu', 'Os02g0103200' => 'osa', 'Os02g0688200' => 'osa', 'Os04g0445300' => 'osa', 'Peaxi162Scf00084g00062' => 'pax', 'Peaxi162Scf00745g00003' => 'pax', 'PGR004G0072' => 'pgr', 'PGSC0003DMG400001717' => 'stu', 'PGSC0003DMG400001728' => 'stu', 'PGSC0003DMG400001844' => 'stu', 'Phvul.003G115000' => 'pvu', 'Phvul.003G227500' => 'pvu', 'Phvul.003G227600' => 'pvu', 'Phvul.003G227700' => 'pvu', 'Phvul.006G071800' => 'pvu', 'Phvul.010G041500' => 'pvu', 'Potri.003G086500' => 'ptr', 'Potri.003G086600' => 'ptr', 'Potri.014G044100' => 'ptr', 'Prupe.2G115600' => 'ppe', 'Prupe.3G007800' => 'ppe', 'Prupe.3G007900' => 'ppe', 'Prupe.5G048600' => 'ppe', 'Prupe.5G048900' => 'ppe', 'Psat4g079960' => 'psa', 'Psat4g080000' => 'psa', 'Psat4g219240' => 'psa', 'PSO017G6871' => 'pso', 'PSO017G7346' => 'pso', 'PSO026G0001' => 'pso', 'PSO081G0031' => 'pso', 'PSO081G0055' => 'pso', 'PSO081G0057' => 'pso', 'PSO081G0137' => 'pso', 'PSO081G0157' => 'pso', 'PSO081G0174' => 'pso', 'PSO081G0177' => 'pso', 'PSO151G0158' => 'pso', 'PSO170G1696' => 'pso', 'PSO170G5213' => 'pso', 'PSO170G5332' => 'pso', 'PSO380G0003' => 'pso', 'PSO384G1724' => 'pso', 'PSO478G2336' => 'pso', 'PSO478G2498' => 'pso', 'PSO478G4988' => 'pso', 'PSO541G1687' => 'pso', 'PSO541G5291' => 'pso', 'PSO541G5973' => 'pso', 'PSO573G0024' => 'pso', 'PSO573G0039' => 'pso', 'PSO675G0940' => 'pso', 'PSO675G1997' => 'pso', 'PSO675G4879' => 'pso', 'PSO775G0001' => 'pso', 'PSO782G0985' => 'pso', 'PSO782G2009' => 'pso', 'PSO782G4131' => 'pso', 'PSO782G4884' => 'pso', 'PSO782G5274' => 'pso', 'PSO832G0663' => 'pso', 'PSO832G1165' => 'pso', 'QL04p026153' => 'qlo', 'QL12p007390' => 'qlo', 'RcHm_v2.0_Chr1g0344001' => 'rch', 'RcHm_v2.0_Chr1g0344031' => 'rch', 'RcHm_v2.0_Chr1g0344051' => 'rch', 'RcHm_v2.0_Chr7g0207981' => 'rch', 'RcHm_v2.0_Chr7g0207991' => 'rch', 'RcHm_v2.0_Chr7g0208011' => 'rch', 'RcHm_v2.0_Chr7g0208771' => 'rch', 'Rhsim01G0143600' => 'rsi', 'Rhsim01G0143700' => 'rsi', 'Rhsim01G0143800' => 'rsi', 'Rhsim11G0009400' => 'rsi', 'Sabra03G0056300' => 'sbr', 'Sabra14G0032000' => 'sbr', 'SalBow4G0032' => 'sbo', 'SalBow5G1724' => 'sbo', 'Sc02g0003280' => 'sci', 'Sc07g0008920' => 'sci', 'Sc07g0008930' => 'sci', 'Sc07g0008940' => 'sci', 'Sc07g0008950' => 'sci', 'Sc08g0009050' => 'sci', 'Sc18g0002750' => 'sci', 'Sc22g0001310' => 'sci', 'Sed0003510' => 'sed', 'Sed0004326' => 'sed', 'Sed0005894' => 'sed', 'Sed0021869' => 'sed', 'Sed0025391' => 'sed', 'Sed0025882' => 'sed', 'SGA_v2.0_scaffold52G19268' => 'sas', 'SGA_v2.0_scaffold77G25252' => 'sas', 'Solyc01g088575.1' => 'sly', 'Solyc01g088590.5' => 'sly', 'Solyc08g077400.3' => 'sly', 'Sopen01g035440' => 'spe', 'Sopen08g025990' => 'spe', 'Sp2g11720' => 'spa', 'Sp2g11730' => 'spa', 'Sp2g11740' => 'spa', 'Sp2g11750' => 'spa', 'Sp2g11760' => 'spa', 'Sp7g03330' => 'spa', 'TAR073G0001' => 'tar', 'TAR375G0055' => 'tar', 'TAR375G0246' => 'tar', 'TAR375G0630' => 'tar', 'TAR375G1152' => 'tar', 'TAR629G2132' => 'tar', 'TAR629G3049' => 'tar', 'THA.LOC104819134' => 'tha', 'THA.LOC104824471' => 'tha', 'Thecc.01G402600' => 'tca', 'Thecc.03G235400' => 'tca', 'Thecc.03G235500' => 'tca', 'Thecc.09G068900' => 'tca', 'Thhalv10001100m.g' => 'esa', 'Thhalv10001105m.g' => 'esa', 'Thhalv10001199m.g' => 'esa', 'Thhalv10027940m.g' => 'esa', 'TPR.G19189' => 'tpr', 'TPR.G39508' => 'tpr', 'TWI14G0207' => 'twi', 'TWI15G1112' => 'twi', 'TWI34G1970' => 'twi', 'TWI56G0141' => 'twi', 'TWI59G0004' => 'twi', 'TWI81G0239' => 'twi', 'TWI81G0308' => 'twi', 'unitig_749.g13774' => 'ugi', 'unitig_750.g28405' => 'ugi', 'vmacro00361' => 'vma', 'vmacro21085' => 'vma', 'vmacro21086' => 'vma', 'vmacro21087' => 'vma', 'VMungo0251G1280' => 'vmu', 'VMungo0251G3442' => 'vmu', 'VMungo0331G1992' => 'vmu', 'VMungo0464G1160' => 'vmu', 'VMungo1215G2168' => 'vmu', 'Zm00001eb229350' => 'zma' ) $gf_id = 'HOM05D001445' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001445' ) $data_identifier = 'HOM05D001445' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'ach' => (int) 5, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 10, 'ath' => (int) 6, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 11, 'can' => (int) 4, 'cansat' => (int) 5, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 1, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 5, 'egr' => (int) 10, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 9, 'han' => (int) 3, 'cav' => (int) 1, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 4, 'lonja' => (int) 1, 'lja' => (int) 4, 'lsa' => (int) 2, 'mes' => (int) 4, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 2, 'cme' => (int) 6, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 3, 'nnu' => (int) 7, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 2, 'pgr' => (int) 1, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 35, 'qlo' => (int) 2, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 2, 'sci' => (int) 8, 'sed' => (int) 6, 'sas' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 2, 'twi' => (int) 7, 'ugi' => (int) 2, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb229350' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 0